Re: [R] 'yum install R' failing with tcl/tk issue

2013-10-29 Thread Michael Stauffer 
Thanks everyone for the replies to my question. The issue turns out to be
that I'm on a Rocks cluster head node, and the Rocks distribution disables
alternate repos by defaut so it's using the Rocks-6.1 repo which has the
old R.

In the meantime I've built R 3.0.2 from source, which seems a better idea
anyway, as I'll need multiple versions of R installed over time.

-M


On Fri, Oct 25, 2013 at 7:43 AM, Marc Schwartz marc_schwa...@me.com wrote:


 On Oct 25, 2013, at 1:29 AM, Prof Brian Ripley rip...@stats.ox.ac.uk
 wrote:

  On 25/10/2013 02:33, Michael Stauffer wrote:
  Hi,
 
  I'm trying to install R on CentOS 6.4.
 
  This is not the right list.  But
 
  - As the posting guide says, we only support current R here.  R 2.10.0
 is ancient, and other people seem to have found 3.0.1 RPMs for Centos 6.3.
 
  - It seems your RPM is linked against Tcl/Tk 8.4, also ancient.  Tcl/Tk
 8.6 is current.
 
  I suggest you install R 3.0.2 from the sources, in which case R-devel
 would be the right list.  For binary installations on CentOS, R-sig-Fedora
 is.
 

 There are several inconsistencies in the output, as 3.0.1 is available as
 an RPM from the EPEL repos:

   http://dl.fedoraproject.org/pub/epel/6/x86_64/repoview/R.html

 In addition, the output below shows that the R rpm being installed is from
 'el5', rather than 'el6'. If this was CentOS 5, rather than 6, R 2.15.2 is
 available:

   http://dl.fedoraproject.org/pub/epel/5/x86_64/repoview/R.html

 Something seems to be amiss with the configuration not getting the right
 yum repo paths.

 A Google search came up with this link:

   http://lancegatlin.org/tech/centos-6-clear-the-yum-cache

 which might be helpful, as it suggests a similar issue of yum picking up
 incorrect versions. You may need to reinstall the EPEL repo RPM after these
 steps.

 Regards,

 Marc Schwartz


 
  Following some instructions online, I've done this:
 
  rpm -Uvh
 
 http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm
 
  yum install R
 
  But yum fails, with this (full output below):
 
  Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
 Requires: libtcl8.4.so()(64bit)
  Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
 Requires: libtk8.4.so()(64bit)
 
  I have tcl/tk 8.5 already installed. Does anyone have any suggestion?
  Thanks!
 
  Full output:
 
  [root@picsl-cluster ~]# yum install R
  Repository base is listed more than once in the configuration
  Rocks-6.1
| 1.9 kB 00:00
  base
 | 3.7 kB 00:00
  Setting up Install Process
  Resolving Dependencies
  -- Running transaction check
  --- Package R.x86_64 0:2.10.0-2.el5 will be installed
  -- Processing Dependency: libRmath-devel = 2.10.0-2.el5 for package:
  R-2.10.0-2.el5.x86_64
  -- Processing Dependency: R-devel = 2.10.0-2.el5 for package:
  R-2.10.0-2.el5.x86_64
  -- Running transaction check
  --- Package R-devel.x86_64 0:2.10.0-2.el5 will be installed
  -- Processing Dependency: R-core = 2.10.0-2.el5 for package:
  R-devel-2.10.0-2.el5.x86_64
  --- Package libRmath-devel.x86_64 0:2.10.0-2.el5 will be installed
  -- Processing Dependency: libRmath = 2.10.0-2.el5 for package:
  libRmath-devel-2.10.0-2.el5.x86_64
  -- Running transaction check
  --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
  -- Processing Dependency: libtk8.4.so()(64bit) for package:
  R-core-2.10.0-2.el5.x86_64
  -- Processing Dependency: libtcl8.4.so()(64bit) for package:
  R-core-2.10.0-2.el5.x86_64
  -- Processing Dependency: libgfortran.so.1()(64bit) for package:
  R-core-2.10.0-2.el5.x86_64
  --- Package libRmath.x86_64 0:2.10.0-2.el5 will be installed
  -- Running transaction check
  --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
  -- Processing Dependency: libtk8.4.so()(64bit) for package:
  R-core-2.10.0-2.el5.x86_64
  -- Processing Dependency: libtcl8.4.so()(64bit) for package:
  R-core-2.10.0-2.el5.x86_64
  --- Package compat-libgfortran-41.x86_64 0:4.1.2-39.el6 will be
 installed
  -- Finished Dependency Resolution
  Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
 Requires: libtcl8.4.so()(64bit)
  Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
 Requires: libtk8.4.so()(64bit)
   You could try using --skip-broken to work around the problem
  ** Found 57 pre-existing rpmdb problem(s), 'yum check' output follows:
  foundation-git-1.7.11.4-0.x86_64 has missing requires of
 perl(SVN::Client)
  foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Core)
  foundation-git-1.7.11.4-0.x86_64 has missing requires of
 perl(SVN::Delta)
  foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Ra)
  1:guestfish-1.7.17-26.el6.x86_64 has missing requires of libguestfs =
 ('1',
  '1.7.17', '26.el6')
  opt-perl-AcePerl-1.92-0.el6.x86_64 has missing requires of
  perl(Ace::Browser::LocalSiteDefs)
  opt-perl-BioPerl-1.6.901-0.el6.noarch has missing

Re: [R] 'yum install R' failing with tcl/tk issue

2013-10-25 Thread Prof Brian Ripley 

On 25/10/2013 02:33, Michael Stauffer wrote:

Hi,

I'm trying to install R on CentOS 6.4.


This is not the right list.  But

- As the posting guide says, we only support current R here.  R 2.10.0 
is ancient, and other people seem to have found 3.0.1 RPMs for Centos 6.3.


- It seems your RPM is linked against Tcl/Tk 8.4, also ancient.  Tcl/Tk 
8.6 is current.


I suggest you install R 3.0.2 from the sources, in which case R-devel 
would be the right list.  For binary installations on CentOS, 
R-sig-Fedora is.




Following some instructions online, I've done this:

rpm -Uvh
http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm

yum install R

But yum fails, with this (full output below):

Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)

I have tcl/tk 8.5 already installed. Does anyone have any suggestion?
Thanks!

Full output:

[root@picsl-cluster ~]# yum install R
Repository base is listed more than once in the configuration
Rocks-6.1
   | 1.9 kB 00:00
base
| 3.7 kB 00:00
Setting up Install Process
Resolving Dependencies
-- Running transaction check
--- Package R.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: libRmath-devel = 2.10.0-2.el5 for package:
R-2.10.0-2.el5.x86_64
-- Processing Dependency: R-devel = 2.10.0-2.el5 for package:
R-2.10.0-2.el5.x86_64
-- Running transaction check
--- Package R-devel.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: R-core = 2.10.0-2.el5 for package:
R-devel-2.10.0-2.el5.x86_64
--- Package libRmath-devel.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: libRmath = 2.10.0-2.el5 for package:
libRmath-devel-2.10.0-2.el5.x86_64
-- Running transaction check
--- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: libtk8.4.so()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
-- Processing Dependency: libtcl8.4.so()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
-- Processing Dependency: libgfortran.so.1()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
--- Package libRmath.x86_64 0:2.10.0-2.el5 will be installed
-- Running transaction check
--- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: libtk8.4.so()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
-- Processing Dependency: libtcl8.4.so()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
--- Package compat-libgfortran-41.x86_64 0:4.1.2-39.el6 will be installed
-- Finished Dependency Resolution
Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)
  You could try using --skip-broken to work around the problem
** Found 57 pre-existing rpmdb problem(s), 'yum check' output follows:
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Client)
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Core)
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Delta)
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Ra)
1:guestfish-1.7.17-26.el6.x86_64 has missing requires of libguestfs = ('1',
'1.7.17', '26.el6')
opt-perl-AcePerl-1.92-0.el6.x86_64 has missing requires of
perl(Ace::Browser::LocalSiteDefs)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Apache::DBI)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::ASN1::EntrezGene)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Expression::Contact)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Expression::DataSet)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Expression::Platform)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Expression::Sample)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Factory)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Forest::Tree)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::IO)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Matrices)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Matrices::Datum)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Matrices::Matrix)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Convert::Binary::C)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(DBD::Pg)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(PostScript::TextBlock)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Test::Exception)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Test::Warn)

Re: [R] 'yum install R' failing with tcl/tk issue

2013-10-25 Thread Milan Bouchet-Valat 
Le jeudi 24 octobre 2013 à 21:33 -0400, Michael Stauffer a écrit :
 Hi,
 
 I'm trying to install R on CentOS 6.4.
 
 Following some instructions online, I've done this:
 
 rpm -Uvh
 http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm
 
 yum install R
 
 But yum fails, with this (full output below):
 
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)
 
 I have tcl/tk 8.5 already installed. Does anyone have any suggestion?
 Thanks!
yum asks for tcl and tk 8.4, so if you have 8.5 it won't work.

You should have told us where you found those instructions. If these are
http://stackoverflow.com/questions/9468164/problems-installing-r-on-linux-centos-6-2
then please try what the poster did there.


Else, I've no idea whether it could work for your system, but the Tcl.Tk
8.4 RPM are available for Fedora 8 here:
ftp://ftp.pbone.net/mirror/archive.fedoraproject.org/fedora/linux/updates/8/x86_64.newkey/tcl-8.4.17-1.fc8.x86_64.rpm
ftp://ftp.pbone.net/mirror/archive.fedoraproject.org/fedora/linux/updates/8/x86_64.newkey/tk-8.4.17-2.fc8.x86_64.rpm



Regards

 Full output:
 
 [root@picsl-cluster ~]# yum install R
 Repository base is listed more than once in the configuration
 Rocks-6.1
   | 1.9 kB 00:00
 base
| 3.7 kB 00:00
 Setting up Install Process
 Resolving Dependencies
 -- Running transaction check
 --- Package R.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libRmath-devel = 2.10.0-2.el5 for package:
 R-2.10.0-2.el5.x86_64
 -- Processing Dependency: R-devel = 2.10.0-2.el5 for package:
 R-2.10.0-2.el5.x86_64
 -- Running transaction check
 --- Package R-devel.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: R-core = 2.10.0-2.el5 for package:
 R-devel-2.10.0-2.el5.x86_64
 --- Package libRmath-devel.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libRmath = 2.10.0-2.el5 for package:
 libRmath-devel-2.10.0-2.el5.x86_64
 -- Running transaction check
 --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libtk8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libtcl8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libgfortran.so.1()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 --- Package libRmath.x86_64 0:2.10.0-2.el5 will be installed
 -- Running transaction check
 --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libtk8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libtcl8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 --- Package compat-libgfortran-41.x86_64 0:4.1.2-39.el6 will be installed
 -- Finished Dependency Resolution
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)
  You could try using --skip-broken to work around the problem
 ** Found 57 pre-existing rpmdb problem(s), 'yum check' output follows:
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Client)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Core)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Delta)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Ra)
 1:guestfish-1.7.17-26.el6.x86_64 has missing requires of libguestfs = ('1',
 '1.7.17', '26.el6')
 opt-perl-AcePerl-1.92-0.el6.x86_64 has missing requires of
 perl(Ace::Browser::LocalSiteDefs)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Apache::DBI)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::ASN1::EntrezGene)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Contact)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::DataSet)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Platform)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Sample)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Factory)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Forest::Tree)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::IO)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Matrices)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Matrices::Datum)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Matrices::Matrix)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Convert::Binary::C)
 opt-perl-BioPerl-1.6.901-0.el6.noarch

Re: [R] 'yum install R' failing with tcl/tk issue

2013-10-25 Thread Marc Schwartz 

On Oct 25, 2013, at 1:29 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote:

 On 25/10/2013 02:33, Michael Stauffer wrote:
 Hi,
 
 I'm trying to install R on CentOS 6.4.
 
 This is not the right list.  But
 
 - As the posting guide says, we only support current R here.  R 2.10.0 is 
 ancient, and other people seem to have found 3.0.1 RPMs for Centos 6.3.
 
 - It seems your RPM is linked against Tcl/Tk 8.4, also ancient.  Tcl/Tk 8.6 
 is current.
 
 I suggest you install R 3.0.2 from the sources, in which case R-devel would 
 be the right list.  For binary installations on CentOS, R-sig-Fedora is.
 

There are several inconsistencies in the output, as 3.0.1 is available as an 
RPM from the EPEL repos:

  http://dl.fedoraproject.org/pub/epel/6/x86_64/repoview/R.html

In addition, the output below shows that the R rpm being installed is from 
'el5', rather than 'el6'. If this was CentOS 5, rather than 6, R 2.15.2 is 
available:

  http://dl.fedoraproject.org/pub/epel/5/x86_64/repoview/R.html

Something seems to be amiss with the configuration not getting the right yum 
repo paths.

A Google search came up with this link:

  http://lancegatlin.org/tech/centos-6-clear-the-yum-cache

which might be helpful, as it suggests a similar issue of yum picking up 
incorrect versions. You may need to reinstall the EPEL repo RPM after these 
steps.

Regards,

Marc Schwartz


 
 Following some instructions online, I've done this:
 
 rpm -Uvh
 http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm
 
 yum install R
 
 But yum fails, with this (full output below):
 
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)
 
 I have tcl/tk 8.5 already installed. Does anyone have any suggestion?
 Thanks!
 
 Full output:
 
 [root@picsl-cluster ~]# yum install R
 Repository base is listed more than once in the configuration
 Rocks-6.1
   | 1.9 kB 00:00
 base
| 3.7 kB 00:00
 Setting up Install Process
 Resolving Dependencies
 -- Running transaction check
 --- Package R.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libRmath-devel = 2.10.0-2.el5 for package:
 R-2.10.0-2.el5.x86_64
 -- Processing Dependency: R-devel = 2.10.0-2.el5 for package:
 R-2.10.0-2.el5.x86_64
 -- Running transaction check
 --- Package R-devel.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: R-core = 2.10.0-2.el5 for package:
 R-devel-2.10.0-2.el5.x86_64
 --- Package libRmath-devel.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libRmath = 2.10.0-2.el5 for package:
 libRmath-devel-2.10.0-2.el5.x86_64
 -- Running transaction check
 --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libtk8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libtcl8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libgfortran.so.1()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 --- Package libRmath.x86_64 0:2.10.0-2.el5 will be installed
 -- Running transaction check
 --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libtk8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libtcl8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 --- Package compat-libgfortran-41.x86_64 0:4.1.2-39.el6 will be installed
 -- Finished Dependency Resolution
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)
  You could try using --skip-broken to work around the problem
 ** Found 57 pre-existing rpmdb problem(s), 'yum check' output follows:
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Client)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Core)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Delta)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Ra)
 1:guestfish-1.7.17-26.el6.x86_64 has missing requires of libguestfs = ('1',
 '1.7.17', '26.el6')
 opt-perl-AcePerl-1.92-0.el6.x86_64 has missing requires of
 perl(Ace::Browser::LocalSiteDefs)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Apache::DBI)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::ASN1::EntrezGene)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Contact)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::DataSet)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Platform)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Sample)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has

Re: [R] 'yum install R' failing with tcl/tk issue

2013-10-24 Thread Pascal Oettli 
Hello,

Do you have headers installed (generally tcl-devel and tk-devel)?

Regards,
Pascal


On 25 October 2013 10:33, Michael Stauffer mgsta...@gmail.com wrote:
 Hi,

 I'm trying to install R on CentOS 6.4.

 Following some instructions online, I've done this:

 rpm -Uvh
 http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm

 yum install R

 But yum fails, with this (full output below):

 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)

 I have tcl/tk 8.5 already installed. Does anyone have any suggestion?
 Thanks!

 Full output:

 [root@picsl-cluster ~]# yum install R
 Repository base is listed more than once in the configuration
 Rocks-6.1
   | 1.9 kB 00:00
 base
| 3.7 kB 00:00
 Setting up Install Process
 Resolving Dependencies
 -- Running transaction check
 --- Package R.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libRmath-devel = 2.10.0-2.el5 for package:
 R-2.10.0-2.el5.x86_64
 -- Processing Dependency: R-devel = 2.10.0-2.el5 for package:
 R-2.10.0-2.el5.x86_64
 -- Running transaction check
 --- Package R-devel.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: R-core = 2.10.0-2.el5 for package:
 R-devel-2.10.0-2.el5.x86_64
 --- Package libRmath-devel.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libRmath = 2.10.0-2.el5 for package:
 libRmath-devel-2.10.0-2.el5.x86_64
 -- Running transaction check
 --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libtk8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libtcl8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libgfortran.so.1()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 --- Package libRmath.x86_64 0:2.10.0-2.el5 will be installed
 -- Running transaction check
 --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libtk8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libtcl8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 --- Package compat-libgfortran-41.x86_64 0:4.1.2-39.el6 will be installed
 -- Finished Dependency Resolution
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)
  You could try using --skip-broken to work around the problem
 ** Found 57 pre-existing rpmdb problem(s), 'yum check' output follows:
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Client)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Core)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Delta)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Ra)
 1:guestfish-1.7.17-26.el6.x86_64 has missing requires of libguestfs = ('1',
 '1.7.17', '26.el6')
 opt-perl-AcePerl-1.92-0.el6.x86_64 has missing requires of
 perl(Ace::Browser::LocalSiteDefs)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Apache::DBI)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::ASN1::EntrezGene)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Contact)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::DataSet)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Platform)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Sample)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Factory)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Forest::Tree)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::IO)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Matrices)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Matrices::Datum)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Matrices::Matrix)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Convert::Binary::C)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(DBD::Pg)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(PostScript::TextBlock)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Test::Exception)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Test::Warn)
 opt-perl-BioPerl-DB-1.006900-0.el6.noarch has missing requires of
 perl(DBD::Oracle)
 opt-perl-BioPerl-Run-1.006900-0.el6.noarch has missing requires of
 perl(Bio::Tools::Run::StandAloneBlastPlus::BlastMethods)